The way I see it is that Naruto has to fight the Bijuu at full strength at some point in the story for the plot's sake. One way of doing this would be giving the Bijuu the Yin chakra of Kurama, as well as the Eight Tails, which is why, for the plot's sake, Naruto didn't get all of Kurama during the sealing.
I think there are 6 flames coming out of the reaper seal... look, there one little coming out a bit under the lowest one... this will be kuramas ying chakra, and narutos godlike pkwer up against jubi